*Target (protein/gene name): Serine Protease NS3 *NCBI Gene # or RefSeq#: 35662466 http://www.ncbi.nlm.nih.gov/protein/3U1I_A *Protein ID (NP or XP #) or Wolbachia#: N/A http://www.rcsb.org/pdb/explore/explore.do?structureId=3U1I *Organism (including strain): Dengue Virus 3 Singapore/8120/1995 http://www.ncbi.nlm.nih.gov/protein/3U1I_A Etiologic Risk Group (see link below): Risk Group 2 (RG2) - Viruses *Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Dengue Virus is a flavivirus carried by mosquitoes and transmitted to monkeys and humans through mosquito bites. Over a third of the wold's population lives in areas at risk for transmission of any of the four strains of Dengue Virus (DENV-1, DENV-2, DENV-3, DENV-4). Dengue transmissions have been high in the recent half century in tropical and subtropical areas; approximately one-hundred-million humans are infected annually. Dengue Virus causes Dengue Fever which may cause high fever, severe headaches and bodily pains, rash, low white cell count, drowsiness, pale skin, breathing difficulties, and mild to severe bleeding. This can be fatal for more extreme cases, especially when the fever becomes hemorrhagic or develops into Dengue shock syndrome. Currently, no vaccines or medications exist for Dengue virus. Analgesics (pain relievers) are suggested, but ibuprofen, Naproxen, and asprin or aspirin containing drugs should be avoided. http://www.cdc.gov/dengue/symptoms/index.html Essentiality of this protein: Yes; essential to maturation of virus. Complex of proteins?: Forms a complex with NS2B to form NS2B(H)-NS3p complex. Druggable Target: Peptide inhibition was effective against Dengue Virus NS3 protease. http://www.sciencedirect.com/science/article/pii/S0006291X05005632
Current Inhibitors: phthalazine-based compound, 7; pthalazine-based compound, 2; quanidine 5; quanidine 4; Bz-NKRR-H Expression Information (has it been expressed in bacterial cells): In E. coli http://www.jbc.org/content/275/14/9963.short
Purification Method: Purified from insoluble inclusion bodies by Ni 2+ ion affinity and gel filtration chromatography. http://www.jbc.org/content/275/14/9963.short Image of protein (PyMol with features delineated and shown separately):
Figure 1: Serine protease nonstructural protein 3 (shown as lines with green carbons, red oxygens, blue nitrogens) found in Dengue Virus covalently bound to a peptide (PDB Identifier: 3u1i). A sulfate ion (red oxygen, yellow sulfur sticks) is the ligand in the active site. *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): http://www.ncbi.nlm.nih.gov/protein/YP_001621843.1
*GC% Content for gene: 46.7% *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
ATG AAC AAT CAA AGA AAA AAG ACA GGA AAG
CCC TCA ATC AAT ATG CTC AAA AGA GTC AGG
AAC AGG GTC AGC ACA GGA AGT CAA CTC GCT
AAA AGA TTC TCT AAA GGA CTG TTG AAC GGA
CAG GGA CCA ATG AAG TTG GTG ATG GCA TTC
ATC GCC TTT CTC AGA TTC CTC GCA ATA CCA
CCT ACA GCA GGG GTC TTA GCA AGA TGG GGA
ACA TTT AAA AAG AGT GGA GCT ATA AAG GTC
CTA AAA GGG TTT AAG AAA GAA ATA TCA AAT
ATG CTG TCC ATA ATT AAT CAG AGA AAA AAG
ACT AGT CTG TGT CTC ATG ATG ATA CTG CCA
GCT GCA CTG GCT TTC CAC CTC ACC TCA AGA
GAC GGA GAG CCA AGA ATG ATC GTG GGA AAA
AAC GAG AGA GGA AAG TCC CTT CTA TTT AAG
ACC GCC TCA GGA ATA AAC ATG TGT ACA CTC
ATC GCA ATG GAT CTT GGA GAA ATG TGC GAT
GAC ACA GTT ACA TAT AAG TGT CCA CAT ATC
ACA GAG GTT GAA CCA GAG GAT ATC GAC TGT
TGG TGT AAT CTC ACT TCA ACT TGG GTG ACT
TAC GGA ACA TGC AAC CAG GCA GGG GAG CAC
AGA AGG GAC AAA AGG AGC GTG GCT CTG GCA
CCA CAC GTG GGC ATG GGA CTC GAT ACC AGG
ACA CAG ACA TGG ATG TCT GCA GAG GGA GCT
TGG AGA CAA GTT GAA AAG GTT GAA ACA TGG
GCC TTG AGA CAT CCA GGA TTT ACC ATT TTG
GCC CTT TTT CTC GCA CAT TAT ATA GGA ACA
TCA CTT ACT CAA AAG GTG GTT ATC TTT ATA
CTC TTA ATG TTG GTG ACA CCA TCA ATG ACA
ATG AGG TGC GTT GGC GTG GGA AAC AGA GAC
TTC GTG GAG GGA CTT AGC GGA GCA ACC TGG
GTG GAT GTT GTC TTG GAA CAT GGC GGA TGC
GTC ACA ACT ATG GCA AAA AAC AAA CCA ACC
CTG GAT ATA GAA CTG CAA AAA ACT GAA GCA
ACT CAG TTG GCT ACA CTA AGA AAA CTA TGC
ATA GAA GGC AAA ATC ACT AAT ATT ACA ACC
GAC TCC AGG TGT CCA ACC CAA GGA GAG GCC
GTG TTA CCA GAG GAA CAG GAT CAA AAT TAT
GTG TGT AAA CAC ACT TAT GTG GAT AGA GGC
TGG GGA AAT GGA TGC GGG CTC TTC GGG AAG
GGC TCT CTC GTC ACA TGC GCA AAG TTC CAA
TGT TTG GAA CCA ATA GAA GGA AAG GTC GTG
CAA TAC GAG AAC CTT AAA TAT ACA GTT ATA
ATT ACA GTG CAC ACA GGA GAT CAA CAC CAG
GTG GGC AAT GAG ACA CAA GGA GTG ACA GCC
GAG ATA ACA CCC CAG GCT TCA ACA ACC GAA
GCA ATA TTG CCC GAA TAC GGA ACT CTG GGA
TTG GAG TGC AGC CCC AGA ACT GGA TTG GAT
TTT AAT GAA ATG ATA TTG CTG ACA ATG AAA
AAC AAG GCC TGG ATG GTC CAC AGA CAA TGG
TTT TTC GAC CTC CCA CTG CCA TGG GCA AGC
GGG GCT ACA ACT GAG ACC CCA ACT TGG AAT
AGG AAA GAA CTC CTT GTT ACA TTC AAA AAT
GCC CAC GCA AAA AAG CAA GAA GTT GTC GTG
CTT GGA AGC CAG GAA GGA GCT ATG CAC ACA
GCT CTC ACA GGG GCT ACA GAG ATA CAA AAC
TCA GGA GGC ACT TCC ATT TTT GCA GGC CAC
TTG AAG TGC AGA TTG AAA ATG GAT AAA CTG
GAA TTA AAG GGA ATG TCA TAC GCC ATG TGT
ACA AAT ACA TTC GTG CTG AAG AAA GAG GTT
AGC GAA ACA CAG CAT GGA ACC ATC TTA ATT
AAG GTG GAA TAT AAA GGA GAA GAC GCT CCT
TGT AAA ATT CCA TTT TCC ACT GAA GAC GGA
CAA GGA AAA GCA CAT AAC GGC AGA CTC ATC
ACC GCA AAT CCC GTG GTT ACA AAA AAG GAA
GAG CCT GTG AAC ATC GAA GCC GAG CCC CCA
TTC GGG GAG AGC AAT ATC GTG ATC GGA ATA
GGA GAC AAT GCA CTA AAA ATT AAT TGG TAT
AAA AAG GGA TCA AGC ATC GGA AAG ATG TTC
GAG GCT ACT GAA AGA GGA GCC AGA AGG ATG
GCC ATT TTG GGA GAT ACA GCA TGG GAC TTC
GGG TCC GTG GGA GGC GTC TTG AAT TCA CTG
GGA AAA ATG GTG CAC CAA ATA TTT GGA TCA
GCA TAT ACT GCA TTG TTC TCA GGA GTC TCA
TGG GTG ATG AAG ATA GGA ATA GGA GTC CTC
TTG ACA TGG ATT GGA CTG AAC TCA AAA AAT
ACA AGT ATG AGT TTC TCC TGT ATA GCT ATT
GGA ATA ATC ACC TTG TAC CTG GGA GCT GTT
GTG CAG GCA GAC ATG GGA TGC GTG ATT AAC
TGG AAA GGC AAA GAA CTG AAG TGC GGA TCT
GGC ATC TTT GTC ACA AAC GAG GTC CAT ACA
TGG ACA GAA CAG TAC AAG TTT CAA GCA GAT
TCA CCA AAA AGA CTC GCT ACT GCT ATT GCT
GGA GCA TGG GAG AAC GGA GTC TGT GGA ATA
AGA AGC ACC ACT AGA ATG GAA AAT TTG TTA
TGG AAG CAA ATA GCA AAT GAA CTG AAT TAT
ATA TTG TGG GAA AAT AAC ATA AAG TTA ACA
GTT GTG GTT GGA GAC ACA CTA GGA GTC CTA
GAA CAA GGA AAA AGG ACA CTG ACA CCT CAA
CCA ATG GAG TTA AAA TAC TCT TGG AAA ACA
TGG GGC AAG GCT AAG ATA GTG ACC GCA GAG
ACA CAG AAT TCA AGC TTC ATT ATA GAC GGC
CCA AAC ACT CCA GAA TGT CCA TCA GCC TCA
AGA GCT TGG AAT GTC TGG GAA GTC GAA GAT
TAC GGG TTC GGG GTC TTT ACC ACA AAT ATC
TGG CTG AAG CTG AGA GAA GTG TAC ACA CAG
TTG TGC GAC CAT AGA TTA ATG TCC GCA GCT
GTT AAG GAC GAG AGA GCA GTT CAC GCC GAC
ATG GGA TAT TGG ATT GAA TCA CAA AAA AAC
GGC TCT TGG AAA CTA GAG AAA GCA TCA CTC
ATC GAG GTG AAA ACT TGC ACA TGG CCA AAA
TCA CAC ACA TTG TGG ACA AAT GGA GTG TTA
GAG TCA GAT ATG ATA ATT CCA AAG TCC CTG
GCT GGG CCA ATT AGT CAA CAT AAC TAT AGA
CCA GGA TAT CAC ACA CAG ACA GCT GGG CCA
TGG CAC TTG GGA AAA CTT GAG TTG GAC TTT
AAT TAT TGT GAA GGG ACC ACT GTG GTT ATT
ACA GAG AGC TGC GGA ACA AGA GGA CCC TCC
CTA AGA ACC ACA ACT GTT TCT GGG AAA TTA
ATA CAC GAA TGG TGT TGC AGA TCA TGT ACA
TTG CCC CCA TTG AGG TAT ATG GGG GAG GAT
GGA TGT TGG TAT GGA ATG GAG ATA AGA CCA
ATA TCT GAA AAG GAG GAA AAC ATG GTT AAA
TCC CTT GTG AGC GCT GGA TCA GGG AAA GTT
GAC AAC TTC ACA ATG GGG GTG TTA TGC TTG
GCT ATT CTT TTT GAG GAA GTG CTA AGA GGA
AAG TTC GGA AAA AAG CAT ATG ATT GCC GGA
GTG TTC TTT ACA TTT GTC CTA TTA CTA TCA
GGG CAA ATA ACA TGG AGA GAC ATG GCA CAT
ACA CTA ATA ATG ATT GGA TCA AAC GCC TCA
GAC AGA ATG GGG ATG GGG GTT ACA TAC CTG
GCA CTG ATT GCA ACA TTT AAA ATT CAA CCA
TTC TTG GCC TTA GGG TTC TTT CTC AGA AAA
TTG ACA TCA AGG GAA AAC CTA TTA CTG GGA
GTC GGC CTG GCA ATG GCT ACA ACC CTA CAA
CTC CCA GAA GAC ATC GAA CAG ATG GCC AAC
GGG GTG GCA CTT GGC CTG ATG GCT CTT AAA
CTT ATA ACA CAA TTC GAA ACA TAT CAG CTT
TGG ACA GCT CTG GTT TCA CTT ACA TGT AGT
AAT ACA ATC TTC ACA CTT ACA GTG GCT TGG
AGA ACA GCC ACA TTG ATT CTA GCA GGA GTT
AGC CTT TTG CCC GTC TGC CAA TCA TCT AGC
ATG AGA AAG ACT GAT TGG TTG CCT ATG ACA
GTG GCT GCC ATG GGA GTG CCT CCA CTG CCT
CTT TTT ATT TTC TCA TTA AAA GAC ACA TTG
AAA AGA AGG TCA TGG CCA TTG AAC GAG GGG
GTT ATG GCA GTC GGA CTC GTG AGT ATC CTA
GCA TCA TCT TTA CTT AGA AAT GAC GTC CCA
ATG GCA GGA CCA TTG GTG GCC GGG GGA CTG
CTT ATT GCC TGC TAC GTC ATA ACA GGA ACT
TCA GCT GAT CTG ACT GTT GAA AAG GCA CCA
GAT GTG ACT TGG GAA GAG GAA GCC GAG CAA
ACA GGA GTC AGC CAT AAC CTA ATG ATA ACT
GTT GAC GAT GAC GGC ACA ATG AGA ATA AAG
GAT GAC GAA ACA GAA AAC ATA CTG ACA GTG
TTG CTG AAA ACA GCA TTG TTA ATC GTT TCT
GGC ATA TTC CCC TAT AGC ATT CCC GCC ACC
TTG TTA GTT TGG CAC ACA TGG CAA AAA CAA
ACC CAA AGA TCT GGA GTG CTG TGG GAC GTG
CCT TCA CCT CCC GAA ACA CAG AAA GCT GAG
CTA GAA GAG GGA GTC TAC AGA ATC AAA CAA
CAG GGG ATA TTT GGG AAA ACA CAA GTC GGC
GTG GGA GTG CAA AAG GAA GGC GTG TTT CAC
ACA ATG TGG CAC GTC ACA AGA GGG GCT GTC
TTG ACA CAT AAC GGA AAG AGA CTG GAG CCT
AAT TGG GCT AGT GTC AAG AAA GAT CTC ATC
AGC TAT GGA GGC GGG TGG AGG TTG TCA GCA
CAG TGG CAG AAG GGA GAG GAA GTG CAA GTG
ATA GCC GTG GAA CCC GGC AAA AAT CCA AAA
AAC TTT CAA ACC ACA CCC GGG ACC TTC CAA
ACA ACT ACA GGA GAA ATT GGG GCA ATA GCC
TTA GAC TTC AAA CCA GGG ACT TCT GGA TCA
CCC ATT ATC AAT AGG GAG GGA AAG GTG GTT
GGA CTG TAC GGC AAC GGA GTG GTT ACA AAG
AAC GGA GGG TAC GTG AGT GGA ATT GCA CAG
ACA AAT GCT GAA CCC GAT GGA CCA ACA CCA
GAA TTG GAG GAA GAG ATG TTT AAA AAG AGA
AAT TTG ACA ATA ATG GAT CTT CAC CCC GGA
TCA GGA AAG ACA AGG AAA TAC CTA CCA GCT
ATA GTG AGA GAA GCT ATA AAA AGG AGA TTG
AGG ACC TTG ATA CTA GCA CCA ACA AGA GTG
GTC GCT GCA GAG ATG GAG GAA GCA CTC AAA
GGA CTC CCT ATC AGG TAC CAG ACA ACT GCC
ACC AAA AGC GAA CAT ACT GGG AGA GAA ATC
GTC GAC TTG ATG TGC CAT GCC ACA TTC ACA
ATG AGA CTC CTA AGC CCC GTG AGG GTG CCA
AAC TAC AAC TTG ATT ATC ATG GAT GAG GCA
CAC TTT ACT GAC CCT GCC TCT ATT GCA GCT
AGA GGG TAT ATA AGC ACA AGA GTG GGG ATG
GGG GAA GCA GCC GCA ATA TTT ATG ACA GCC
ACA CCA CCT GGA ACT GCT GAT GCA TTC CCT
CAG TCA AAC GCC CCA ATA CAG GAT GAG GAA
AGA GAT ATC CCA GAA AGA TCA TGG AAC TCA
GGA AAT GAA TGG ATT ACA GAC TTC GCT GGC
AAG ACA GTG TGG TTT GTG CCA TCA ATT AAG
GCT GGC AAT GAC ATC GCC AAC TGT CTT AGA
AAG AAC GGA AAA AAG GTG ATA CAG CTA TCA
AGG AAA ACC TTC GAT ACA GAA TAC CAA AAG
ACA AAG CTG AAC GAT TGG GAC TTT GTT GTG
ACA ACC GAC ATA TCT GAA ATG GGA GCC AAC
TTC AAG GCA GAC AGA GTG ATA GAT CCA AGG
AGA TGC TTG AAA CCT GTG ATA TTA ACA GAC
GGA CCT GAG AGA GTT ATC CTA GCT GGC CCA
ATG CCC GTG ACC GCC GCA TCA GCC GCT CAG
AGA AGG GGA AGG GTG GGA AGA AAC CCA CAA
AAA GAG AAT GAT CAA TAC ATC TTT ACC GGA
CAA CCT CTG AAC AAT GAC GAG GAC CAC GCT
CAT TGG ACA GAA GCA AAA ATG TTG CTC GAC
AAC ATT AAT ACT CCT GAG GGC ATT ATC CCC
GCC CTC TTT GAA CCT GAG AGA GAA AAG AGT
GCA GCT ATC GAC GGA GAG TAC AGG TTA AAA
GGA GAG TCA AGA AAA ACC TTC GTT GAA CTC
ATG AGG AGA GGC GAC TTA CCA GTC TGG TTG
GCA CAC AAA GTG GCC AGT GAA GGG ATA AAG
TAC ACA GAC AGA AAA TGG TGT TTC GAT GGA
CAA AGA AAC AAT CAG ATA CTC GAA GAG AAC
ATG GAC GTG GAA ATC TGG ACA AAA GAG GGA
GAA AAG AAA AAG CTA AGA CCA AGA TGG CTT
GAC GCT AGA ACA TAC TCA GAC CCT CTC GCC
CTT AAA GAA TTT AAA GAT TTT GCA GCT GGA
AGA AAA TCC ATA GCA CTC GAT CTG GTC ACA
GAG ATA GGG AGG GTC CCA TCA CAT TTG GCA
CAT AGG ACC AGA AAC GCT CTT GAT AAT CTG
GTG ATG CTA CAC ACC TCA GAA GAT GGA GGG
AGG GCA TAC AGG CAC GCC GTT GAG GAA TTA
CCC GAA ACA ATG GAA ACC CTC TTA CTG CTA
GGA TTA ATG ATA CTA CTG ACA GGC GGA GCA
ATG TTG TTT TTG ATT TCA GGG AAA GGA ATA
GGA AAA ACA AGC ATA GGG CTT ATA TGT GTG
ATA GCC TCA TCT GGA ATG CTT TGG ATG GCA
GAG GTG CCA CTA CAA TGG ATA GCC TCA GCA
ATC GTG CTT GAA TTT TTC ATG ATG GTG CTG
TTG ATA CCT GAA CCA GAA AAG CAA AGA ACA
CCA CAA GAC AAC CAA TTA GCA TAC GTT GTC
ATC GGA ATA TTG ACA TTA GCC GCA ACT ATA
GCC GCA AAC GAG ATG GGG CTA CTG GAG ACA
ACT AAA AGA GAT CTT GGG ATG TCC AAA GAA
CCA GGG GTT GTC TCC CCT ACA TCT TAC CTA
GAT GTG GAC CTA CAT CCT GCA TCT GCA TGG
ACA CTC TAT GCC GTT GCA ACC ACA GTG ATT
ACC CCA ATG TTA AGG CAT ACC ATC GAA AAC
TCT ACA GCC AAC GTG TCC CTA GCT GCA ATC
GCA AAC CAG GCC GTT GTG CTG ATG GGA TTA
GAT AAG GGC TGG CCA ATT AGT AAA ATG GAT
CTC GGA GTC CCC TTG CTA GCC CTG GGA TGC
TAT TCT CAG GTT AAT CCA TTA ACA TTA ACA
GCC GCT GTT CTC CTA CTT ATA ACC CAC TAC
GCA ATC ATA GGA CCA GGC CTG CAA GCC AAG
GCT ACA AGA GAA GCT CAA AAG AGA ACA GCA
GCT GGA ATT ATG AAA AAC CCA ACA GTG GAC
GGA ATC ATG ACA ATA GAT TTG GAT TCA GTC
ATT TTC GAT AGT AAA TTT GAG AAA CAG CTG
GGA CAA GTG ATG TTA CTC GTG CTT TGC GCT
GTT CAA CTT TTG CTA ATG AGA ACA TCC TGG
GCT TTG TGC GAG GCA TTA ACA TTG GCA ACT
GGA CCC ATA ACT ACA CTG TGG GAA GGA TCC
CCT GGG AAG TTC TGG AAC ACA ACC ATA GCA
GTG TCA ATG GCA AAC ATT TTT AGG GGA TCC
TAC TTG GCA GGA GCT GGA CTG GCC TTC TCC
ATT ATG AAA TCC GTT GGA ACC GGC AAA AGA
GGA ACC GGA TCA CAA GGA GAA ACA TTA GGA
GAA AAG TGG AAA AAG AAA TTG AAC CAA CTC
TCA AGA AAA GAA TTC GAT TTG TAT AAA AAG
TCA GGA ATT ACA GAA GTG GAC AGA ACA GAG
GCA AAG GAA GGC CTC AAG AGA GGA GAA ACA
ACT CAC CAT GCT GTC TCA AGG GGA TCA GCA
AAG TTA CAA TGG TTT GTC GAA AGA AAC ATG
GTG GTT CCA GAA GGC AGA GTG ATT GAC TTG
GGG TGT GGC AGA GGA GGG TGG TCA TAT TAC
TGC GCA GGG CTG AAA AAG GTG ACA GAG GTG
AGA GGA TAT ACA AAA GGA GGG CCA GGA CAT
GAA GAG CCA GTG CCA ATG TCC ACA TAC GGA
TGG AAC ATA GTC AAG TTA ATG AGT GGA AAA
GAC GTC TTC TAC CTA CCA CCC GAG AAA TGT
GAC ACC CTA CTT TGT GAT ATT GGC GAA TCA
TCT CCA TCT CCA ACA GTG GAA GAG AGC AGA
ACA ATT AGA GTG CTT AAA ATG GTG GAG CCA
TGG CTA AAA AAT AAC CAA TTT TGC ATT AAA
GTC CTT AAT CCA TAC ATG CCA ACA GTG ATC
GAA CAC CTG GAG AGG TTG CAG AGG AAA CAT
GGA GGC ATG CTT GTG AGA AAC CCA CTG TCA
AGA AAC AGC ACT CAT GAA ATG TAC TGG ATT
TCA AAC GGA ACA GGA AAC ATT GTT TCA AGC
GTT AAC ATG GTG TCC AGA CTG TTA CTT AAT
AGA TTT ACA ATG ACA CAC AGA AGG CCC ACA
ATT GAA AAA GAC GTG GAC CTA GGA GCC GGA
ACC AGA CAC GTG AAC GCA GAG CCC GAA ACA
CCT AAT ATG GAT GTG ATA GGG GAG AGG ATA
AAA AGA ATC AAA GAA GAG CAC AAC TCA ACA
TGG CAT TAT GAC GAT GAA AAC CCT TAT AAA
ACT TGG GCC TAC CAC GGA AGT TAT GAA GTT
AAG GCA ACA GGC AGT GCC TCT TCC ATG ATT
AAC GGA GTG GTT AAA TTG CTC ACT AAA CCT
TGG GAC GTG GTT CCA ATG GTT ACA CAA ATG
GCT ATG ACA GAC ACA ACC CCC TTT GGA CAA
CAG AGG GTC TTC AAG GAA AAG GTC GAC ACT
AGG ACC CCC AGA CCA ATG CCA GGA ACA AGG
AAA GCA ATG GAA ATA ACA GCA GAA TGG TTG
TGG AGA ACC CTG GGA AGA AAT AAA AGA CCA
AGG TTA TGC ACC AGA GAG GAA TTC ACA AAG
AAA GTG AGA ACA AAC GCA GCT ATG GGA GCA
GTG TTC ACA GAA GAG AAC CAA TGG GAC TCA
GCA AAA GCA GCC GTG GAA GAT GAA GAG TTT
TGG AAA CTC GTG GAT AGA GAA AGA GAA CTT
CAT AAA CTG GGA AAA TGT GGC TCA TGT GTG
TAC AAT ATG ATG GGA AAG AGA GAG AAG AAA
CTC GGA GAA TTC GGC AAG GCT AAA GGG TCA
AGG GCC ATT TGG TAT ATG TGG TTA GGG GCC
AGA TAC TTG GAA TTC GAG GCT CTA GGA TTT
CTT AAC GAA GAC CAC TGG TTC AGT AGG GAG
AAC TCA TAC TCA GGA GTG GAA GGA GAG GGA
CTG CAT AAA CTC GGA TAC ATT CTT AGA GAC
ATA AGT AAG ATA CCA GGA GGG GCC ATG TAC
GCA GAC GAT ACT GCA GGG TGG GAT ACA AGA
ATT ACA GAA GAC GAT CTG CAT AAC GAG GAA
AAA ATA ATC CAA CAG ATG GAC CCC GAA CAC
AGA CAA CTT GCT AAC GCC ATT TTT AAA CTA
ACT TAC CAA AAC AAG GTG GTC AAA GTC CAA
AGA CCA ACC CCT ACA GGA ACC GTT ATG GAC
ATA ATT TCC AGA AAG GAT CAG AGA GGC TCT
GGA CAA TTG GGA ACA TAC GGC TTG AAT ACC
TTT ACA AAC ATG GAA GCA CAA CTT GTG AGA
CAA ATG GAA GGG GAA GGG GTG CTG ACA AAA
GCT GAC TTG GAA AAC CCA CAT TTA CTA GAG
AAG AAA ATC ACA CAA TGG TTG GAA ACA AAG
GGA GTG GAG AGA CTG AAG AGA ATG GCT ATA
TCA GGC GAT GAC TGT GTG GTT AAG CCT ATA
GAC GAT AGG TTT GCC AAT GCA CTG CTC GCC
CTG AAT GAC ATG GGA AAG GTG AGA AAG GAT
ATT CCA CAA TGG CAA CCA TCA AAA GGG TGG
CAC GAT TGG CAA CAG GTG CCA TTT TGT AGC
CAC CAT TTC CAT GAG CTG ATA ATG AAA GAC
GGC AGA AAA TTA GTG GTC CCT TGT AGA CCA
CAA GAT GAG CTC ATA GGG AGA GCC AGA ATT
AGC CAG GGA GCC GGC TGG TCT CTG AGA GAG
ACT GCA TGT CTG GGA AAA GCC TAC GCA CAA
ATG TGG TCA CTG ATG TAT TTC CAC AGA AGG
GAC CTC AGA TTA GCA TCC AAT GCA ATA TGC
AGC GCA GTG CCA GTG CAC TGG GTG CCA ACA
TCA AGA ACA ACT TGG TCC ATA CAC GCC CAC
CAT CAA TGG ATG ACA ACA GAG GAC ATG CTG
ACA GTG TGG AAT AGA GTG TGG ATT GAA GAG
AAT CCA TGG ATG GAA GAT AAA ACA CCA GTC
ACA ACA TGG GAA AAC GTG CCA TAC TTG GGG
AAA AGA GAG GAT CAA TGG TGC GGA TCA CTC
ATA GGC TTG ACA TCC AGA GCA ACA TGG GCA
CAA AAC ATC CCA ACA GCC ATA CAG CAA GTG
AGA TCA CTT ATC GGG AAT GAG GAA TTT CTC
GAC TAC ATG CCC AGC ATG AAG AGA TTC AGA
AAG GAG GAA GAG TCT GAG GGG GCC ATT TGG
TAA
*GC% Content for gene (codon optimized):
60.06%
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
*NCBI Gene # or RefSeq#: 35662466
http://www.ncbi.nlm.nih.gov/protein/3U1I_A
*Protein ID (NP or XP #) or Wolbachia#: N/A
http://www.rcsb.org/pdb/explore/explore.do?structureId=3U1I
*Organism (including strain): Dengue Virus 3 Singapore/8120/1995
http://www.ncbi.nlm.nih.gov/protein/3U1I_A
Etiologic Risk Group (see link below): Risk Group 2 (RG2) - Viruses
*Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Dengue Virus is a flavivirus carried by mosquitoes and transmitted to monkeys and humans through mosquito bites. Over a third of the wold's population lives in areas at risk for transmission of any of the four strains of Dengue Virus (DENV-1, DENV-2, DENV-3, DENV-4). Dengue transmissions have been high in the recent half century in tropical and subtropical areas; approximately one-hundred-million humans are infected annually. Dengue Virus causes Dengue Fever which may cause high fever, severe headaches and bodily pains, rash, low white cell count, drowsiness, pale skin, breathing difficulties, and mild to severe bleeding. This can be fatal for more extreme cases, especially when the fever becomes hemorrhagic or develops into Dengue shock syndrome. Currently, no vaccines or medications exist for Dengue virus. Analgesics (pain relievers) are suggested, but ibuprofen, Naproxen, and asprin or aspirin containing drugs should be avoided.
http://www.cdc.gov/dengue/symptoms/index.html
Essentiality of this protein: Yes; essential to maturation of virus.
Complex of proteins?: Forms a complex with NS2B to form NS2B(H)-NS3p complex.
Druggable Target: Peptide inhibition was effective against Dengue Virus NS3 protease.
http://www.sciencedirect.com/science/article/pii/S0006291X05005632
*EC#: 3.4.21.91, 3.6.1.15, 3.6.4.13 (Multiple EC#'s listed)
Link to BRENDA EC# page: (In order of EC# respectively)
http://brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.91
http://brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.15
http://brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): Chromogenic and Fluorescent assay
http://www.sciencedirect.com/science/article/pii/S0006291X05005632
-- link to Sigma (or other company) page for assay or assay reagents (substrates) - Currently unavailable
-- link (or citation) to paper that contains assay information
http://brenda-enzymes.info/literature/lit.php4?e=3.4.21.91&r=682978
http://www.sciencedirect.com/science/article/pii/S0006291X05005632
-- List cost and quantity of substrate reagents and supplier - N/A, see above
Structure Available (PDB or Homology model)
PDB: 3u1i
Current Inhibitors: phthalazine-based compound, 7; pthalazine-based compound, 2; quanidine 5; quanidine 4; Bz-NKRR-H
Expression Information (has it been expressed in bacterial cells): In E. coli
http://www.jbc.org/content/275/14/9963.short
Purification Method: Purified from insoluble inclusion bodies by Ni 2+ ion affinity and gel filtration chromatography.
http://www.jbc.org/content/275/14/9963.short
Image of protein (PyMol with features delineated and shown separately):
Figure 1: Serine protease nonstructural protein 3 (shown as lines with green carbons, red oxygens, blue nitrogens) found in Dengue Virus covalently bound to a peptide (PDB Identifier: 3u1i). A sulfate ion (red oxygen, yellow sulfur sticks) is the ligand in the active site.
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
http://www.ncbi.nlm.nih.gov/protein/YP_001621843.1
1 mnnqrkktgk psinmlkrvr nrvstgsqla krfskgllng qgpmklvmaf iaflrflaip 61 ptagvlarwg tfkksgaikv lkgfkkeisn mlsiinqrkk tslclmmilp aalafhltsr 121 dgeprmivgk nergksllfk tasginmctl iamdlgemcd dtvtykcphi tevepedidc 181 wcnltstwvt ygtcnqageh rrdkrsvala phvgmgldtr tqtwmsaega wrqvekvetw 241 alrhpgftil alflahyigt sltqkvvifi llmlvtpsmt mrcvgvgnrd fveglsgatw 301 vdvvlehggc vttmaknkpt ldielqktea tqlatlrklc iegkitnitt dsrcptqgea 361 vlpeeqdqny vckhtyvdrg wgngcglfgk gslvtcakfq clepiegkvv qyenlkytvi 421 itvhtgdqhq vgnetqgvta eitpqastte ailpeygtlg lecsprtgld fnemilltmk 481 nkawmvhrqw ffdlplpwas gattetptwn rkellvtfkn ahakkqevvv lgsqegamht 541 altgateiqn sggtsifagh lkcrlkmdkl elkgmsyamc tntfvlkkev setqhgtili 601 kveykgedap ckipfstedg qgkahngrli tanpvvtkke epvnieaepp fgesnivigi 661 gdnalkinwy kkgssigkmf eatergarrm ailgdtawdf gsvggvlnsl gkmvhqifgs 721 aytalfsgvs wvmkigigvl ltwiglnskn tsmsfsciai giitlylgav vqadmgcvin 781 wkgkelkcgs gifvtnevht wteqykfqad spkrlataia gawengvcgi rsttrmenll 841 wkqianelny ilwenniklt vvvgdtlgvl eqgkrtltpq pmelkyswkt wgkakivtae 901 tqnssfiidg pntpecpsas rawnvweved ygfgvfttni wlklrevytq lcdhrlmsaa 961 vkderavhad mgywiesqkn gswklekasl ievktctwpk shtlwtngvl esdmiipksl 1021 agpisqhnyr pgyhtqtagp whlgkleldf nycegttvvi tescgtrgps lrtttvsgkl 1081 ihewccrsct lpplrymged gcwygmeirp isekeenmvk slvsagsgkv dnftmgvlcl 1141 ailfeevlrg kfgkkhmiag vfftfvllls gqitwrdmah tlimigsnas drmgmgvtyl 1201 aliatfkiqp flalgfflrk ltsrenlllg vglamattlq lpedieqman gvalglmalk 1261 litqfetyql wtalvsltcs ntiftltvaw rtatlilagv sllpvcqsss mrktdwlpmt 1321 vaamgvpplp lfifslkdtl krrswplneg vmavglvsil assllrndvp magplvaggl 1381 liacyvitgt sadltvekap dvtweeeaeq tgvshnlmit vdddgtmrik ddeteniltv 1441 llktallivs gifpysipat llvwhtwqkq tqrsgvlwdv psppetqkae leegvyrikq 1501 qgifgktqvg vgvqkegvfh tmwhvtrgav lthngkrlep nwasvkkdli sygggwrlsa 1561 qwqkgeevqv iavepgknpk nfqttpgtfq tttgeigaia ldfkpgtsgs piinregkvv 1621 glygngvvtk nggyvsgiaq tnaepdgptp eleeemfkkr nltimdlhpg sgktrkylpa 1681 ivreaikrrl rtlilaptrv vaaemeealk glpiryqtta tksehtgrei vdlmchatft 1741 mrllspvrvp nynliimdea hftdpasiaa rgyistrvgm geaaaifmta tppgtadafp 1801 qsnapiqdee rdiperswns gnewitdfag ktvwfvpsik agndianclr kngkkviqls 1861 rktfdteyqk tklndwdfvv ttdisemgan fkadrvidpr rclkpviltd gpervilagp 1921 mpvtaasaaq rrgrvgrnpq kendqyiftg qplnndedha hwteakmlld nintpegiip 1981 alfepereks aaidgeyrlk gesrktfvel mrrgdlpvwl ahkvasegik ytdrkwcfdg 2041 qrnnqileen mdveiwtkeg ekkklrprwl dartysdpla lkefkdfaag rksialdlvt 2101 eigrvpshla hrtrnaldnl vmlhtsedgg rayrhaveel petmetllll glmilltgga 2161 mlflisgkgi gktsiglicv iassgmlwma evplqwiasa ivleffmmvl lipepekqrt 2221 pqdnqlayvv igiltlaati aanemgllet tkrdlgmske pgvvsptsyl dvdlhpasaw 2281 tlyavattvi tpmlrhtien stanvslaai anqavvlmgl dkgwpiskmd lgvpllalgc 2341 ysqvnpltlt aavlllithy aiigpglqak atreaqkrta agimknptvd gimtidldsv 2401 ifdskfekql gqvmllvlca vqlllmrtsw alcealtlat gpittlwegs pgkfwnttia 2461 vsmanifrgs ylagaglafs imksvgtgkr gtgsqgetlg ekwkkklnql srkefdlykk 2521 sgitevdrte akeglkrget thhavsrgsa klqwfvernm vvpegrvidl gcgrggwsyy 2581 caglkkvtev rgytkggpgh eepvpmstyg wnivklmsgk dvfylppekc dtllcdiges 2641 spsptveesr tirvlkmvep wlknnqfcik vlnpymptvi ehlerlqrkh ggmlvrnpls 2701 rnsthemywi sngtgnivss vnmvsrllln rftmthrrpt iekdvdlgag trhvnaepet 2761 pnmdvigeri krikeehnst whyddenpyk twayhgsyev katgsassmi ngvvklltkp 2821 wdvvpmvtqm amtdttpfgq qrvfkekvdt rtprpmpgtr kameitaewl wrtlgrnkrp 2881 rlctreeftk kvrtnaamga vfteenqwds akaavedeef wklvdrerel hklgkcgscv 2941 ynmmgkrekk lgefgkakgs raiwymwlga rylefealgf lnedhwfsre nsysgvegeg 3001 lhklgyilrd iskipggamy addtagwdtr iteddlhnee kiiqqmdpeh rqlanaifkl 3061 tyqnkvvkvq rptptgtvmd iisrkdqrgs gqlgtyglnt ftnmeaqlvr qmegegvltk 3121 adlenphlle kkitqwletk gverlkrmai sgddcvvkpi ddrfanalla lndmgkvrkd 3181 ipqwqpskgw hdwqqvpfcs hhfhelimkd grklvvpcrp qdeligrari sqgagwslre 3241 taclgkayaq mwslmyfhrr dlrlasnaic savpvhwvpt srttwsihah hqwmttedml 3301 tvwnrvwiee npwmedktpv ttwenvpylg kredqwcgsl igltsratwa qniptaiqqv 3361 rsligneefl dympsmkrfr keeesegaiw*length of your protein in Amino Acids: 3391 Amino AcidsMolecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 818568.5 kDa
Molar Extinction coefficient of your protein at 280 nm wavelength: 130500 1/(Mcm)
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html): N/A
*CDS Gene Sequence (paste as text only):
http://www.ncbi.nlm.nih.gov/nuccore/NC_001475.2?report=fasta&from=95&to=10267
*GC% Content for gene: 46.7%
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
ATG AAC AAT CAA AGA AAA AAG ACA GGA AAG
CCC TCA ATC AAT ATG CTC AAA AGA GTC AGG
AAC AGG GTC AGC ACA GGA AGT CAA CTC GCT
AAA AGA TTC TCT AAA GGA CTG TTG AAC GGA
CAG GGA CCA ATG AAG TTG GTG ATG GCA TTC
ATC GCC TTT CTC AGA TTC CTC GCA ATA CCA
CCT ACA GCA GGG GTC TTA GCA AGA TGG GGA
ACA TTT AAA AAG AGT GGA GCT ATA AAG GTC
CTA AAA GGG TTT AAG AAA GAA ATA TCA AAT
ATG CTG TCC ATA ATT AAT CAG AGA AAA AAG
ACT AGT CTG TGT CTC ATG ATG ATA CTG CCA
GCT GCA CTG GCT TTC CAC CTC ACC TCA AGA
GAC GGA GAG CCA AGA ATG ATC GTG GGA AAA
AAC GAG AGA GGA AAG TCC CTT CTA TTT AAG
ACC GCC TCA GGA ATA AAC ATG TGT ACA CTC
ATC GCA ATG GAT CTT GGA GAA ATG TGC GAT
GAC ACA GTT ACA TAT AAG TGT CCA CAT ATC
ACA GAG GTT GAA CCA GAG GAT ATC GAC TGT
TGG TGT AAT CTC ACT TCA ACT TGG GTG ACT
TAC GGA ACA TGC AAC CAG GCA GGG GAG CAC
AGA AGG GAC AAA AGG AGC GTG GCT CTG GCA
CCA CAC GTG GGC ATG GGA CTC GAT ACC AGG
ACA CAG ACA TGG ATG TCT GCA GAG GGA GCT
TGG AGA CAA GTT GAA AAG GTT GAA ACA TGG
GCC TTG AGA CAT CCA GGA TTT ACC ATT TTG
GCC CTT TTT CTC GCA CAT TAT ATA GGA ACA
TCA CTT ACT CAA AAG GTG GTT ATC TTT ATA
CTC TTA ATG TTG GTG ACA CCA TCA ATG ACA
ATG AGG TGC GTT GGC GTG GGA AAC AGA GAC
TTC GTG GAG GGA CTT AGC GGA GCA ACC TGG
GTG GAT GTT GTC TTG GAA CAT GGC GGA TGC
GTC ACA ACT ATG GCA AAA AAC AAA CCA ACC
CTG GAT ATA GAA CTG CAA AAA ACT GAA GCA
ACT CAG TTG GCT ACA CTA AGA AAA CTA TGC
ATA GAA GGC AAA ATC ACT AAT ATT ACA ACC
GAC TCC AGG TGT CCA ACC CAA GGA GAG GCC
GTG TTA CCA GAG GAA CAG GAT CAA AAT TAT
GTG TGT AAA CAC ACT TAT GTG GAT AGA GGC
TGG GGA AAT GGA TGC GGG CTC TTC GGG AAG
GGC TCT CTC GTC ACA TGC GCA AAG TTC CAA
TGT TTG GAA CCA ATA GAA GGA AAG GTC GTG
CAA TAC GAG AAC CTT AAA TAT ACA GTT ATA
ATT ACA GTG CAC ACA GGA GAT CAA CAC CAG
GTG GGC AAT GAG ACA CAA GGA GTG ACA GCC
GAG ATA ACA CCC CAG GCT TCA ACA ACC GAA
GCA ATA TTG CCC GAA TAC GGA ACT CTG GGA
TTG GAG TGC AGC CCC AGA ACT GGA TTG GAT
TTT AAT GAA ATG ATA TTG CTG ACA ATG AAA
AAC AAG GCC TGG ATG GTC CAC AGA CAA TGG
TTT TTC GAC CTC CCA CTG CCA TGG GCA AGC
GGG GCT ACA ACT GAG ACC CCA ACT TGG AAT
AGG AAA GAA CTC CTT GTT ACA TTC AAA AAT
GCC CAC GCA AAA AAG CAA GAA GTT GTC GTG
CTT GGA AGC CAG GAA GGA GCT ATG CAC ACA
GCT CTC ACA GGG GCT ACA GAG ATA CAA AAC
TCA GGA GGC ACT TCC ATT TTT GCA GGC CAC
TTG AAG TGC AGA TTG AAA ATG GAT AAA CTG
GAA TTA AAG GGA ATG TCA TAC GCC ATG TGT
ACA AAT ACA TTC GTG CTG AAG AAA GAG GTT
AGC GAA ACA CAG CAT GGA ACC ATC TTA ATT
AAG GTG GAA TAT AAA GGA GAA GAC GCT CCT
TGT AAA ATT CCA TTT TCC ACT GAA GAC GGA
CAA GGA AAA GCA CAT AAC GGC AGA CTC ATC
ACC GCA AAT CCC GTG GTT ACA AAA AAG GAA
GAG CCT GTG AAC ATC GAA GCC GAG CCC CCA
TTC GGG GAG AGC AAT ATC GTG ATC GGA ATA
GGA GAC AAT GCA CTA AAA ATT AAT TGG TAT
AAA AAG GGA TCA AGC ATC GGA AAG ATG TTC
GAG GCT ACT GAA AGA GGA GCC AGA AGG ATG
GCC ATT TTG GGA GAT ACA GCA TGG GAC TTC
GGG TCC GTG GGA GGC GTC TTG AAT TCA CTG
GGA AAA ATG GTG CAC CAA ATA TTT GGA TCA
GCA TAT ACT GCA TTG TTC TCA GGA GTC TCA
TGG GTG ATG AAG ATA GGA ATA GGA GTC CTC
TTG ACA TGG ATT GGA CTG AAC TCA AAA AAT
ACA AGT ATG AGT TTC TCC TGT ATA GCT ATT
GGA ATA ATC ACC TTG TAC CTG GGA GCT GTT
GTG CAG GCA GAC ATG GGA TGC GTG ATT AAC
TGG AAA GGC AAA GAA CTG AAG TGC GGA TCT
GGC ATC TTT GTC ACA AAC GAG GTC CAT ACA
TGG ACA GAA CAG TAC AAG TTT CAA GCA GAT
TCA CCA AAA AGA CTC GCT ACT GCT ATT GCT
GGA GCA TGG GAG AAC GGA GTC TGT GGA ATA
AGA AGC ACC ACT AGA ATG GAA AAT TTG TTA
TGG AAG CAA ATA GCA AAT GAA CTG AAT TAT
ATA TTG TGG GAA AAT AAC ATA AAG TTA ACA
GTT GTG GTT GGA GAC ACA CTA GGA GTC CTA
GAA CAA GGA AAA AGG ACA CTG ACA CCT CAA
CCA ATG GAG TTA AAA TAC TCT TGG AAA ACA
TGG GGC AAG GCT AAG ATA GTG ACC GCA GAG
ACA CAG AAT TCA AGC TTC ATT ATA GAC GGC
CCA AAC ACT CCA GAA TGT CCA TCA GCC TCA
AGA GCT TGG AAT GTC TGG GAA GTC GAA GAT
TAC GGG TTC GGG GTC TTT ACC ACA AAT ATC
TGG CTG AAG CTG AGA GAA GTG TAC ACA CAG
TTG TGC GAC CAT AGA TTA ATG TCC GCA GCT
GTT AAG GAC GAG AGA GCA GTT CAC GCC GAC
ATG GGA TAT TGG ATT GAA TCA CAA AAA AAC
GGC TCT TGG AAA CTA GAG AAA GCA TCA CTC
ATC GAG GTG AAA ACT TGC ACA TGG CCA AAA
TCA CAC ACA TTG TGG ACA AAT GGA GTG TTA
GAG TCA GAT ATG ATA ATT CCA AAG TCC CTG
GCT GGG CCA ATT AGT CAA CAT AAC TAT AGA
CCA GGA TAT CAC ACA CAG ACA GCT GGG CCA
TGG CAC TTG GGA AAA CTT GAG TTG GAC TTT
AAT TAT TGT GAA GGG ACC ACT GTG GTT ATT
ACA GAG AGC TGC GGA ACA AGA GGA CCC TCC
CTA AGA ACC ACA ACT GTT TCT GGG AAA TTA
ATA CAC GAA TGG TGT TGC AGA TCA TGT ACA
TTG CCC CCA TTG AGG TAT ATG GGG GAG GAT
GGA TGT TGG TAT GGA ATG GAG ATA AGA CCA
ATA TCT GAA AAG GAG GAA AAC ATG GTT AAA
TCC CTT GTG AGC GCT GGA TCA GGG AAA GTT
GAC AAC TTC ACA ATG GGG GTG TTA TGC TTG
GCT ATT CTT TTT GAG GAA GTG CTA AGA GGA
AAG TTC GGA AAA AAG CAT ATG ATT GCC GGA
GTG TTC TTT ACA TTT GTC CTA TTA CTA TCA
GGG CAA ATA ACA TGG AGA GAC ATG GCA CAT
ACA CTA ATA ATG ATT GGA TCA AAC GCC TCA
GAC AGA ATG GGG ATG GGG GTT ACA TAC CTG
GCA CTG ATT GCA ACA TTT AAA ATT CAA CCA
TTC TTG GCC TTA GGG TTC TTT CTC AGA AAA
TTG ACA TCA AGG GAA AAC CTA TTA CTG GGA
GTC GGC CTG GCA ATG GCT ACA ACC CTA CAA
CTC CCA GAA GAC ATC GAA CAG ATG GCC AAC
GGG GTG GCA CTT GGC CTG ATG GCT CTT AAA
CTT ATA ACA CAA TTC GAA ACA TAT CAG CTT
TGG ACA GCT CTG GTT TCA CTT ACA TGT AGT
AAT ACA ATC TTC ACA CTT ACA GTG GCT TGG
AGA ACA GCC ACA TTG ATT CTA GCA GGA GTT
AGC CTT TTG CCC GTC TGC CAA TCA TCT AGC
ATG AGA AAG ACT GAT TGG TTG CCT ATG ACA
GTG GCT GCC ATG GGA GTG CCT CCA CTG CCT
CTT TTT ATT TTC TCA TTA AAA GAC ACA TTG
AAA AGA AGG TCA TGG CCA TTG AAC GAG GGG
GTT ATG GCA GTC GGA CTC GTG AGT ATC CTA
GCA TCA TCT TTA CTT AGA AAT GAC GTC CCA
ATG GCA GGA CCA TTG GTG GCC GGG GGA CTG
CTT ATT GCC TGC TAC GTC ATA ACA GGA ACT
TCA GCT GAT CTG ACT GTT GAA AAG GCA CCA
GAT GTG ACT TGG GAA GAG GAA GCC GAG CAA
ACA GGA GTC AGC CAT AAC CTA ATG ATA ACT
GTT GAC GAT GAC GGC ACA ATG AGA ATA AAG
GAT GAC GAA ACA GAA AAC ATA CTG ACA GTG
TTG CTG AAA ACA GCA TTG TTA ATC GTT TCT
GGC ATA TTC CCC TAT AGC ATT CCC GCC ACC
TTG TTA GTT TGG CAC ACA TGG CAA AAA CAA
ACC CAA AGA TCT GGA GTG CTG TGG GAC GTG
CCT TCA CCT CCC GAA ACA CAG AAA GCT GAG
CTA GAA GAG GGA GTC TAC AGA ATC AAA CAA
CAG GGG ATA TTT GGG AAA ACA CAA GTC GGC
GTG GGA GTG CAA AAG GAA GGC GTG TTT CAC
ACA ATG TGG CAC GTC ACA AGA GGG GCT GTC
TTG ACA CAT AAC GGA AAG AGA CTG GAG CCT
AAT TGG GCT AGT GTC AAG AAA GAT CTC ATC
AGC TAT GGA GGC GGG TGG AGG TTG TCA GCA
CAG TGG CAG AAG GGA GAG GAA GTG CAA GTG
ATA GCC GTG GAA CCC GGC AAA AAT CCA AAA
AAC TTT CAA ACC ACA CCC GGG ACC TTC CAA
ACA ACT ACA GGA GAA ATT GGG GCA ATA GCC
TTA GAC TTC AAA CCA GGG ACT TCT GGA TCA
CCC ATT ATC AAT AGG GAG GGA AAG GTG GTT
GGA CTG TAC GGC AAC GGA GTG GTT ACA AAG
AAC GGA GGG TAC GTG AGT GGA ATT GCA CAG
ACA AAT GCT GAA CCC GAT GGA CCA ACA CCA
GAA TTG GAG GAA GAG ATG TTT AAA AAG AGA
AAT TTG ACA ATA ATG GAT CTT CAC CCC GGA
TCA GGA AAG ACA AGG AAA TAC CTA CCA GCT
ATA GTG AGA GAA GCT ATA AAA AGG AGA TTG
AGG ACC TTG ATA CTA GCA CCA ACA AGA GTG
GTC GCT GCA GAG ATG GAG GAA GCA CTC AAA
GGA CTC CCT ATC AGG TAC CAG ACA ACT GCC
ACC AAA AGC GAA CAT ACT GGG AGA GAA ATC
GTC GAC TTG ATG TGC CAT GCC ACA TTC ACA
ATG AGA CTC CTA AGC CCC GTG AGG GTG CCA
AAC TAC AAC TTG ATT ATC ATG GAT GAG GCA
CAC TTT ACT GAC CCT GCC TCT ATT GCA GCT
AGA GGG TAT ATA AGC ACA AGA GTG GGG ATG
GGG GAA GCA GCC GCA ATA TTT ATG ACA GCC
ACA CCA CCT GGA ACT GCT GAT GCA TTC CCT
CAG TCA AAC GCC CCA ATA CAG GAT GAG GAA
AGA GAT ATC CCA GAA AGA TCA TGG AAC TCA
GGA AAT GAA TGG ATT ACA GAC TTC GCT GGC
AAG ACA GTG TGG TTT GTG CCA TCA ATT AAG
GCT GGC AAT GAC ATC GCC AAC TGT CTT AGA
AAG AAC GGA AAA AAG GTG ATA CAG CTA TCA
AGG AAA ACC TTC GAT ACA GAA TAC CAA AAG
ACA AAG CTG AAC GAT TGG GAC TTT GTT GTG
ACA ACC GAC ATA TCT GAA ATG GGA GCC AAC
TTC AAG GCA GAC AGA GTG ATA GAT CCA AGG
AGA TGC TTG AAA CCT GTG ATA TTA ACA GAC
GGA CCT GAG AGA GTT ATC CTA GCT GGC CCA
ATG CCC GTG ACC GCC GCA TCA GCC GCT CAG
AGA AGG GGA AGG GTG GGA AGA AAC CCA CAA
AAA GAG AAT GAT CAA TAC ATC TTT ACC GGA
CAA CCT CTG AAC AAT GAC GAG GAC CAC GCT
CAT TGG ACA GAA GCA AAA ATG TTG CTC GAC
AAC ATT AAT ACT CCT GAG GGC ATT ATC CCC
GCC CTC TTT GAA CCT GAG AGA GAA AAG AGT
GCA GCT ATC GAC GGA GAG TAC AGG TTA AAA
GGA GAG TCA AGA AAA ACC TTC GTT GAA CTC
ATG AGG AGA GGC GAC TTA CCA GTC TGG TTG
GCA CAC AAA GTG GCC AGT GAA GGG ATA AAG
TAC ACA GAC AGA AAA TGG TGT TTC GAT GGA
CAA AGA AAC AAT CAG ATA CTC GAA GAG AAC
ATG GAC GTG GAA ATC TGG ACA AAA GAG GGA
GAA AAG AAA AAG CTA AGA CCA AGA TGG CTT
GAC GCT AGA ACA TAC TCA GAC CCT CTC GCC
CTT AAA GAA TTT AAA GAT TTT GCA GCT GGA
AGA AAA TCC ATA GCA CTC GAT CTG GTC ACA
GAG ATA GGG AGG GTC CCA TCA CAT TTG GCA
CAT AGG ACC AGA AAC GCT CTT GAT AAT CTG
GTG ATG CTA CAC ACC TCA GAA GAT GGA GGG
AGG GCA TAC AGG CAC GCC GTT GAG GAA TTA
CCC GAA ACA ATG GAA ACC CTC TTA CTG CTA
GGA TTA ATG ATA CTA CTG ACA GGC GGA GCA
ATG TTG TTT TTG ATT TCA GGG AAA GGA ATA
GGA AAA ACA AGC ATA GGG CTT ATA TGT GTG
ATA GCC TCA TCT GGA ATG CTT TGG ATG GCA
GAG GTG CCA CTA CAA TGG ATA GCC TCA GCA
ATC GTG CTT GAA TTT TTC ATG ATG GTG CTG
TTG ATA CCT GAA CCA GAA AAG CAA AGA ACA
CCA CAA GAC AAC CAA TTA GCA TAC GTT GTC
ATC GGA ATA TTG ACA TTA GCC GCA ACT ATA
GCC GCA AAC GAG ATG GGG CTA CTG GAG ACA
ACT AAA AGA GAT CTT GGG ATG TCC AAA GAA
CCA GGG GTT GTC TCC CCT ACA TCT TAC CTA
GAT GTG GAC CTA CAT CCT GCA TCT GCA TGG
ACA CTC TAT GCC GTT GCA ACC ACA GTG ATT
ACC CCA ATG TTA AGG CAT ACC ATC GAA AAC
TCT ACA GCC AAC GTG TCC CTA GCT GCA ATC
GCA AAC CAG GCC GTT GTG CTG ATG GGA TTA
GAT AAG GGC TGG CCA ATT AGT AAA ATG GAT
CTC GGA GTC CCC TTG CTA GCC CTG GGA TGC
TAT TCT CAG GTT AAT CCA TTA ACA TTA ACA
GCC GCT GTT CTC CTA CTT ATA ACC CAC TAC
GCA ATC ATA GGA CCA GGC CTG CAA GCC AAG
GCT ACA AGA GAA GCT CAA AAG AGA ACA GCA
GCT GGA ATT ATG AAA AAC CCA ACA GTG GAC
GGA ATC ATG ACA ATA GAT TTG GAT TCA GTC
ATT TTC GAT AGT AAA TTT GAG AAA CAG CTG
GGA CAA GTG ATG TTA CTC GTG CTT TGC GCT
GTT CAA CTT TTG CTA ATG AGA ACA TCC TGG
GCT TTG TGC GAG GCA TTA ACA TTG GCA ACT
GGA CCC ATA ACT ACA CTG TGG GAA GGA TCC
CCT GGG AAG TTC TGG AAC ACA ACC ATA GCA
GTG TCA ATG GCA AAC ATT TTT AGG GGA TCC
TAC TTG GCA GGA GCT GGA CTG GCC TTC TCC
ATT ATG AAA TCC GTT GGA ACC GGC AAA AGA
GGA ACC GGA TCA CAA GGA GAA ACA TTA GGA
GAA AAG TGG AAA AAG AAA TTG AAC CAA CTC
TCA AGA AAA GAA TTC GAT TTG TAT AAA AAG
TCA GGA ATT ACA GAA GTG GAC AGA ACA GAG
GCA AAG GAA GGC CTC AAG AGA GGA GAA ACA
ACT CAC CAT GCT GTC TCA AGG GGA TCA GCA
AAG TTA CAA TGG TTT GTC GAA AGA AAC ATG
GTG GTT CCA GAA GGC AGA GTG ATT GAC TTG
GGG TGT GGC AGA GGA GGG TGG TCA TAT TAC
TGC GCA GGG CTG AAA AAG GTG ACA GAG GTG
AGA GGA TAT ACA AAA GGA GGG CCA GGA CAT
GAA GAG CCA GTG CCA ATG TCC ACA TAC GGA
TGG AAC ATA GTC AAG TTA ATG AGT GGA AAA
GAC GTC TTC TAC CTA CCA CCC GAG AAA TGT
GAC ACC CTA CTT TGT GAT ATT GGC GAA TCA
TCT CCA TCT CCA ACA GTG GAA GAG AGC AGA
ACA ATT AGA GTG CTT AAA ATG GTG GAG CCA
TGG CTA AAA AAT AAC CAA TTT TGC ATT AAA
GTC CTT AAT CCA TAC ATG CCA ACA GTG ATC
GAA CAC CTG GAG AGG TTG CAG AGG AAA CAT
GGA GGC ATG CTT GTG AGA AAC CCA CTG TCA
AGA AAC AGC ACT CAT GAA ATG TAC TGG ATT
TCA AAC GGA ACA GGA AAC ATT GTT TCA AGC
GTT AAC ATG GTG TCC AGA CTG TTA CTT AAT
AGA TTT ACA ATG ACA CAC AGA AGG CCC ACA
ATT GAA AAA GAC GTG GAC CTA GGA GCC GGA
ACC AGA CAC GTG AAC GCA GAG CCC GAA ACA
CCT AAT ATG GAT GTG ATA GGG GAG AGG ATA
AAA AGA ATC AAA GAA GAG CAC AAC TCA ACA
TGG CAT TAT GAC GAT GAA AAC CCT TAT AAA
ACT TGG GCC TAC CAC GGA AGT TAT GAA GTT
AAG GCA ACA GGC AGT GCC TCT TCC ATG ATT
AAC GGA GTG GTT AAA TTG CTC ACT AAA CCT
TGG GAC GTG GTT CCA ATG GTT ACA CAA ATG
GCT ATG ACA GAC ACA ACC CCC TTT GGA CAA
CAG AGG GTC TTC AAG GAA AAG GTC GAC ACT
AGG ACC CCC AGA CCA ATG CCA GGA ACA AGG
AAA GCA ATG GAA ATA ACA GCA GAA TGG TTG
TGG AGA ACC CTG GGA AGA AAT AAA AGA CCA
AGG TTA TGC ACC AGA GAG GAA TTC ACA AAG
AAA GTG AGA ACA AAC GCA GCT ATG GGA GCA
GTG TTC ACA GAA GAG AAC CAA TGG GAC TCA
GCA AAA GCA GCC GTG GAA GAT GAA GAG TTT
TGG AAA CTC GTG GAT AGA GAA AGA GAA CTT
CAT AAA CTG GGA AAA TGT GGC TCA TGT GTG
TAC AAT ATG ATG GGA AAG AGA GAG AAG AAA
CTC GGA GAA TTC GGC AAG GCT AAA GGG TCA
AGG GCC ATT TGG TAT ATG TGG TTA GGG GCC
AGA TAC TTG GAA TTC GAG GCT CTA GGA TTT
CTT AAC GAA GAC CAC TGG TTC AGT AGG GAG
AAC TCA TAC TCA GGA GTG GAA GGA GAG GGA
CTG CAT AAA CTC GGA TAC ATT CTT AGA GAC
ATA AGT AAG ATA CCA GGA GGG GCC ATG TAC
GCA GAC GAT ACT GCA GGG TGG GAT ACA AGA
ATT ACA GAA GAC GAT CTG CAT AAC GAG GAA
AAA ATA ATC CAA CAG ATG GAC CCC GAA CAC
AGA CAA CTT GCT AAC GCC ATT TTT AAA CTA
ACT TAC CAA AAC AAG GTG GTC AAA GTC CAA
AGA CCA ACC CCT ACA GGA ACC GTT ATG GAC
ATA ATT TCC AGA AAG GAT CAG AGA GGC TCT
GGA CAA TTG GGA ACA TAC GGC TTG AAT ACC
TTT ACA AAC ATG GAA GCA CAA CTT GTG AGA
CAA ATG GAA GGG GAA GGG GTG CTG ACA AAA
GCT GAC TTG GAA AAC CCA CAT TTA CTA GAG
AAG AAA ATC ACA CAA TGG TTG GAA ACA AAG
GGA GTG GAG AGA CTG AAG AGA ATG GCT ATA
TCA GGC GAT GAC TGT GTG GTT AAG CCT ATA
GAC GAT AGG TTT GCC AAT GCA CTG CTC GCC
CTG AAT GAC ATG GGA AAG GTG AGA AAG GAT
ATT CCA CAA TGG CAA CCA TCA AAA GGG TGG
CAC GAT TGG CAA CAG GTG CCA TTT TGT AGC
CAC CAT TTC CAT GAG CTG ATA ATG AAA GAC
GGC AGA AAA TTA GTG GTC CCT TGT AGA CCA
CAA GAT GAG CTC ATA GGG AGA GCC AGA ATT
AGC CAG GGA GCC GGC TGG TCT CTG AGA GAG
ACT GCA TGT CTG GGA AAA GCC TAC GCA CAA
ATG TGG TCA CTG ATG TAT TTC CAC AGA AGG
GAC CTC AGA TTA GCA TCC AAT GCA ATA TGC
AGC GCA GTG CCA GTG CAC TGG GTG CCA ACA
TCA AGA ACA ACT TGG TCC ATA CAC GCC CAC
CAT CAA TGG ATG ACA ACA GAG GAC ATG CTG
ACA GTG TGG AAT AGA GTG TGG ATT GAA GAG
AAT CCA TGG ATG GAA GAT AAA ACA CCA GTC
ACA ACA TGG GAA AAC GTG CCA TAC TTG GGG
AAA AGA GAG GAT CAA TGG TGC GGA TCA CTC
ATA GGC TTG ACA TCC AGA GCA ACA TGG GCA
CAA AAC ATC CCA ACA GCC ATA CAG CAA GTG
AGA TCA CTT ATC GGG AAT GAG GAA TTT CTC
GAC TAC ATG CCC AGC ATG AAG AGA TTC AGA
AAG GAG GAA GAG TCT GAG GGG GCC ATT TGG
TAA
*GC% Content for gene (codon optimized):
60.06%
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
http://www.ncbi.nlm.nih.gov/protein/3U1I_A
http://europepmc.org/abstract/MED/18674567
http://www.sciencedirect.com/science/article/pii/S0006291X05005632
http://www.sciencedirect.com/science/article/pii/S0960894X05012291